Gene-based Pathogen Identification

microbiome-pathogen-detection-from-nanopore-foodborne-data/gene-based-pathogen-identification

Author(s)
Engy Nasr, Bérénice Batut, Paul Zierep
version Version
2
last_modification Last updated
Jun 7, 2024
license License
MIT
galaxy-tags Tags
name:Collection
name:PathoGFAIR
name:IWC
name:microGalaxy

Features
Tutorial
hands_on Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition
workflow Other workflows associated with this material
Workflow Testing
Tests: ✅
Results: Not yet automated
FAIRness purl PURL
https://gxy.io/GTN:W00142
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on WorkflowHub
Launch in Tutorial Mode question
galaxy-download Download
flowchart TD
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Inputs

Input Label
Input dataset collection collection_of_preprocessed_samples

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2 Extract element identifiers
__BUILD_LIST__ Build list
toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0 Split file
toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.1+galaxy0 Flye
param_value_from_file Parse parameter value
toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.7.2+galaxy0 medaka consensus pipeline
toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4 Bandage Image
toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1 FASTA-to-Tabular
toolshed.g2.bx.psu.edu/repos/iuc/abricate/abricate/1.0.1 ABRicate
toolshed.g2.bx.psu.edu/repos/iuc/abricate/abricate/1.0.1 ABRicate
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4 Replace
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4 Replace
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4 Replace
toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1 Tabular-to-FASTA

Tools

Tool Links
__BUILD_LIST__
param_value_from_file
toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.1+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/abricate/abricate/1.0.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.7.2+galaxy0 View in ToolShed

To use these workflows in Galaxy you can either click the links to download the workflows, or you can right-click and copy the link to the workflow which can be used in the Galaxy form to import workflows.

Importing into Galaxy

Below are the instructions for importing these workflows directly into your Galaxy server of choice to start using them!
Hands-on: Importing a workflow
  • Click on Workflow on the top menu bar of Galaxy. You will see a list of all your workflows.
  • Click on galaxy-upload Import at the top-right of the screen
  • Provide your workflow
    • Option 1: Paste the URL of the workflow into the box labelled “Archived Workflow URL”
    • Option 2: Upload the workflow file in the box labelled “Archived Workflow File”
  • Click the Import workflow button

Below is a short video demonstrating how to import a workflow from GitHub using this procedure:

Video: Importing a workflow from URL

Version History

Version Commit Time Comments
2 cdd93376a 2024-06-06 12:00:29 adding tags to some of the workflow outputs, updating the training with the latest PathoGFAIR workflows updates
1 c63ce23c7 2024-05-26 12:29:47 updating workflows file names

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/workflows/gene_based_pathogen_identification.ga -O workflow.ga
workflow-to-tools -w workflow.ga -o tools.yaml
shed-tools install -g GALAXY -a API_KEY -t tools.yaml
workflow-install -g GALAXY -a API_KEY -w workflow.ga --publish-workflows